fafb_world_mapper: Convert coordinates between different FAFB assemblies

Description Usage Arguments Examples

View source: R/fafb_mapper.R

Description

fafb_world_mapper provides a low-level interface to map coordinates based on the tem-services API available from inside the HHMI Janelia VPN. The hope is to make this service generally available in due course.

End users are not presently expected to use this directly. Instead they should use xform_brain to transform data. See examples.

Usage

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fafb_world_mapper(
  xyz,
  from,
  to,
  baseurl = paste0("http://tem-services.int.janelia.org:8080/render-ws/v1/",
    "owner/flyTEM/project/FAFB00/stack"),
  method = c("single", "many"),
  ...
)

Arguments

xyz

xyz coordinates (in nm)

from, to

Assemblies to convert between e.g. "v12", "v13", "v14".

baseurl

path to Janelia tem-services server (not externally visible at the moment)

method

Whether to try and convert multiple coordinates at once. Defaults to 'single'. The 'many' method currently appears fragile and not much faster.

...

Additional arguments (currently unused)

Examples

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## Not run: 
FAFB12.surf=xform_brain(JFRC2013.surf, sample = JFRC2013, reference = FAFB12)
FAFB13.surf=xform_brain(JFRC2013.surf, sample=JFRC2013, ref=FAFB13)
# current assembly
FAFB.surf=xform_brain(JFRC2013.surf, sample=JFRC2013, ref=FAFB)

## End(Not run)

jefferis/elmr documentation built on Feb. 23, 2020, 7:50 p.m.